gnu: linux-libre 5.4: Update to 5.4.165.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.165.
(linux-libre-5.4-pristine-source): Update hash.

gnu: linux-libre 5.10: Update to 5.10.85.

* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.85.
(linux-libre-5.10-pristine-source): Update hash.

gnu: linux-libre: Update to 5.15.8.

* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.8.
(linux-libre-5.15-pristine-source): Update hash.

gnu: php: Disable yet another failing test.

* gnu/packages/php.scm (php)[arguments]: Delete the
openssl_x509_checkpurpose_basic.phpt test.

gnu: chrony: Update to 4.2.

* gnu/packages/ntp.scm (chrony): Update to 4.2.
[arguments]: Don't explicitly return #t from phases.

gnu: dpkg: Update to 1.21.0.

* gnu/packages/debian.scm (dpkg): Update to 1.21.0.
[arguments]: Don't explicitly return #t from phases.

gnu: Add r-shinyhelper.

* gnu/packages/cran.scm (r-shinyhelper): New variable.

gnu: java-log4j-api: Update to 2.16.0.

This is a follow-up release because of an incorrect fix to
CVE-2021-45046.

* gnu/packages/java.scm (java-log4j-api): Update to 2.16.0.

gnu: emacs-eacl: Update to 2.2.0.

* gnu/packages/emacs-xyz.scm (emacs-eacl): Update to 2.2.0.

gnu: manuskript: Update to 0.13.1.

* gnu/packages/text-editors.scm (manuskript): Update to 0.13.1.

gnu: Add cl-april.

* gnu/packages/lisp-xyz.scm (sbcl-april, cl-april, ecl-april): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-simple-date-time.

* gnu/packages/lisp-xyz.scm (sbcl-simple-date-time, cl-simple-date-time,
  ecl-simple-date-time): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-decimals.

* gnu/packages/lisp-xyz.scm (sbcl-decimals, cl-decimals, ecl-decimals):
  New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-random-state.

* gnu/packages/lisp-xyz.scm (sbcl-random-state, cl-random-state,
  ecl-random-state): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: Add cl-maxpc.

* gnu/packages/lisp-xyz.scm (sbcl-maxpc, cl-maxpc, ecl-maxpc): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: python-pyflow: Rename to python2-pyflow.

The package was never compatible with Python 3. Not adding a deprecated
package variant, because going from Python 3 to Python 2 is a breaking
change and it’s unlikely anyone ever used the package anyway (it was
likely broken).

* gnu/packages/python-science.scm (python-pyflow): Move…
(python2-pyflow): …here.
[arguments]: Use Python 2.

gnu: python-flask-restful: Rewrite import.

It seems a function inside python-flask moved to a different module.

* gnu/packages/python-web.scm (python-flask-restful)[arguments]: Add
phase rewriting imports from flask.helpers to flask.scaffold.

gnu: Add js-mathjax-3.

* gnu/packages/javascript.scm (js-mathjax-3): New variable.
* gnu/packages/patches/mathjax-disable-webpack.patch,
gnu/packages/patches/mathjax-no-a11y.patch: New patches.
* gnu/local.mk (dist_patch_DATA): Register them.

gnu: Add todoman.

* gnu/packages/task-management.scm (todoman): New variable.

gnu: Replace JUPYTER_CONFIG_DIR with JUPYTER_CONFIG_PATH.

Judging by the documentation
(https://jupyter.readthedocs.io/en/latest/use/jupyter-directories.html)
_DIR can only be a single value, whereas _PATH supports :-delimited
values and extends _DIR with extra directories.

* gnu/packages/python-xyz.scm (python-jupyter-core)[native-search-paths]:
Replace _DIR with _PATH.
(python-nbconvert)[arguments]: Unset JUPYTER_CONFIG_PATH during tests.
(python-notebook)[arguments]: Dito.